Commit 3c2f04e2-cb86-43c7-9993-d7882c0899a7/main - fastaq

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~~.gitignore~~ less more

0		*.py[cod]
1
2		# C extensions
3		*.so
4
5		# Packages
6		*.egg
7		*.egg-info
8		dist
9		build
10		eggs
11		parts
12		bin
13		var
14		sdist
15		develop-eggs
16		.installed.cfg
17		lib
18		lib64
19
20		# Installer logs
21		pip-log.txt
22
23		# Unit test / coverage reports
24		.coverage
25		.tox
26		nosetests.xml
27
28		# Translations
29		*.mo
30
31		# Mr Developer
32		.mr.developer.cfg
33		.project
34		.pydevproject

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~~.travis.yml~~ less more

0		language: python
1		python:
2		- "3.4"
3		sudo: false
4		script:
5		- "python setup.py test"

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PKG-INFO less more

	0	Metadata-Version: 2.1
	1	Name: pyfastaq
	2	Version: 3.17.0
	3	Summary: Script to manipulate FASTA and FASTQ files, plus API for developers
	4	Home-page: https://github.com/sanger-pathogens/Fastaq
	5	Author: Martin Hunt
	6	Author-email: path-help@sanger.ac.uk
	7	License: GPLv3
	8	Platform: UNKNOWN
	9	Classifier: Development Status :: 4 - Beta
	10	Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
	11	Classifier: Programming Language :: Python :: 3 :: Only
	12	Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
	13	License-File: LICENSE
	14	License-File: AUTHORS
	15
	16	UNKNOWN
	17

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README.md less more

0		Fastaq
1		======
	0	# Fastaq
	1	Manipulate FASTA and FASTQ files
2	2
	3	[![Build Status](https://travis-ci.org/sanger-pathogens/Fastaq.svg?branch=master)](https://travis-ci.org/sanger-pathogens/Fastaq)
	4	[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg)](https://github.com/sanger-pathogens/Fastaq/blob/master/LICENSE)
	5
	6	## Contents
	7	* [Introduction](#introduction)
	8	* [Installation](#installation)
	9	* [Using pip3](#using-pip3)
	10	* [From source](#from-source)
	11	* [Running the tests](#running-the-tests)
	12	* [Usage](#usage)
	13	* [Examples](#examples)
	14	* [Available commands](#available-commands)
	15	* [For developers](#for-developers)
	16	* [License](#license)
	17	* [Feedback/Issues](#feedbackissues)
	18
	19	## Introduction
3	20	Python3 script to manipulate FASTA and FASTQ (and other format) files, plus API for developers
4	21
5		Installation
6		------------
	22	## Installation
	23	There are a number of ways to install Fastaq and details are provided below. If you encounter an issue when installing Fastaq please contact your local system administrator. If you encounter a bug please log it [here](https://github.com/sanger-pathogens/Fastaq/issues) or email us at path-help@sanger.ac.uk.
7	24
8		Install with pip3:
	25	### Using pip3
9	26
10		pip3 install pyfastaq
	27	`pip3 install pyfastaq`
11	28
	29	### From source
12	30
13		Alternatively, you can download the latest release from this github repository,
14		or clone the repository. Then run the tests:
	31	Download the latest release from this github repository or clone the repository. Then run the tests:
15	32
16		python3 setup.py test
	33	`python3 setup.py test`
17	34
18	35	If the tests all pass, install:
19	36
20		python3 setup.py install
	37	`python3 setup.py install`
21	38
	39	### Running the tests
22	40
23		Usage
24		-----
	41	The test can be run from the top level directory:
	42
	43	`python3 setup.py test`
	44
	45	### Runtime dependencies
	46
	47	These must be available in your path at run time:
	48	* samtools 0.1.19
	49	* gzip
	50	* gunzip
	51
	52	## Usage
25	53
26	54	The installation will put a single script called `fastaq` in your path.
27	55	The usage is:
28	56
29		fastaq <command> [options]
30
	57	`fastaq <command> [options]`
31	58
32	59	Key points:
33	60	* To list the available commands and brief descriptions, just run `fastaq`

39	66	* Input and output files can be gzipped. An input file is assumed to be gzipped if its name ends with .gz. To gzip an output file, just name it with .gz at the end.
40	67	* You can use a minus sign for a filename to use stdin or stdout, so commands can be piped together. See the example below.
41	68
42
43		Examples
44		--------
	69	### Examples
45	70
46	71	Reverse complement all sequences in a file:
47	72
48		fastaq reverse_complement in.fastq out.fastq
	73	`fastaq reverse_complement in.fastq out.fastq`
49	74
50	75	Reverse complement all sequences in a gzipped file, then translate each sequence:
51	76
52		fastaq reverse_complement in.fastq.gz - \| fastaq translate - out.fasta
	77	`fastaq reverse_complement in.fastq.gz - \| fastaq translate - out.fasta`
53	78
54	79
55		Available commands
56		------------------
	80	### Available commands
57	81
58	82	\| Command \| Description \|
59	83	\|-----------------------\|----------------------------------------------------------------------\|

97	121	\| version \| Print version number and exit \|
98	122
99	123
100		For developers
101		--------------
	124	### For developers
102	125
103	126	Here is a template for counting the sequences in a FASTA or FASTQ file:
104
105		from pyfastaq import sequences
106		seq_reader = sequences.file_reader(infile)
107		count = 0
108		for seq in seq_reader:
109		count += 1
110		print(count)
111
	127	```
	128	from pyfastaq import sequences
	129	seq_reader = sequences.file_reader(infile)
	130	count = 0
	131	for seq in seq_reader:
	132	count += 1
	133	print(count)
	134	```
112	135	Hopefully you get the idea and there are plenty of examples in tasks.py. Detection of the input file type and whether gzipped or not is automatic. See help(sequences) for the various methods already defined in the classes Fasta and Fastq.
113	136
114		---------------------------------
	137	## License
	138	Fastaq is free software, licensed under [GPLv3](https://github.com/sanger-pathogens/Fastaq/blob/master/LICENSE).
115	139
116		Build status: [![Build Status](https://travis-ci.org/sanger-pathogens/Fastaq.svg?branch=master)](https://travis-ci.org/sanger-pathogens/Fastaq)
117
118
	140	## Feedback/Issues
	141	Please report any issues to the [issues page](https://github.com/sanger-pathogens/Fastaq/issues) or email path-help@sanger.ac.uk.

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debian/changelog less more

	0	fastaq (3.17.0+git20211102.1.3a993b9-1) UNRELEASED; urgency=low
	1
	2	* New upstream snapshot.
	3
	4	-- Debian Janitor <janitor@jelmer.uk> Sat, 13 Nov 2021 00:14:36 -0000
	5
0	6	fastaq (3.17.0-4) unstable; urgency=medium
1	7
2	8	[ Steffen Moeller ]

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pyfastaq/runners/filter.py less more

9	9	parser.add_argument('--regex', help='If given, only reads with a name matching the regular expression will be kept')
10	10	parser.add_argument('--ids_file', help='If given, only reads whose ID is in th given file will be used. One ID per line of file.', metavar='FILENAME')
11	11	parser.add_argument('-v', '--invert', action='store_true', help='Only keep sequences that do not match the filters')
	12	parser.add_argument('--check_comments', action='store_true', help='Search the header comments also for the given regex. Can only be specified with --regex')
12	13
13	14	mate_group = parser.add_argument_group('Mate file for read pairs options')
14	15	mate_group.add_argument('--mate_in', help='Name of mates input file. If used, must also provide --mate_out', metavar='FILENAME')

28	29	mate_in=options.mate_in,
29	30	mate_out=options.mate_out,
30	31	both_mates_pass=options.both_mates_pass,
	32	check_comments=options.check_comments,
31	33	)

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pyfastaq/tasks.py less more

4	4	from pyfastaq import sequences, utils, caf
5	5
6	6	class Error (Exception): pass
	7
	8
	9	class IncompatibleParametersError(Exception):
	10	pass
	11
7	12
8	13	def acgtn_only(infile, outfile):
9	14	'''Replace every non-acgtn (case insensitve) character with an N'''

283	288	mate_in=None,
284	289	mate_out=None,
285	290	both_mates_pass=True,
	291	check_comments=False
286	292	):
	293	if check_comments and not regex:
	294	raise IncompatibleParametersError(
	295	"--check_comments can only be passed with --regex"
	296	)
287	297
288	298	ids_from_file = set()
289	299	if ids_file is not None:

308	318	def passes(seq, name_regex):
309	319	# remove trailing comments from FASTQ readname lines
310	320	matches = name_regex.match(seq.id)
311		if matches is not None:
	321	if matches is not None and not check_comments:
312	322	clean_seq_id = matches.group(1)
313	323	else:
314	324	clean_seq_id = seq.id

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~~pyfastaq/tests/data/caf_test.caf~~ less more

0
1		DNA : read1.p1k
2		NACG
3		TAN
4
5		BaseQuality : read1.p1k
6		4 24 42 43 40 30 8
7
8		Sequence : read1.p1k
9		Is_read
10		SCF_File read1.p1kSCF
11		Template read1
12		Insert_size 2000 4000
13		Ligation_no 12345
14		Primer Universal_primer
15		Strand Forward
16		Dye Dye_terminator
17		Clone clone1
18		Seq_vec SVEC 1 15 puc19
19		Sequencing_vector "puc19"
20		Clipping QUAL 2 6
21		ProcessStatus PASS
22		Asped 2006-7-5
23		Unpadded
24		Align_to_SCF 1 1272 1 1272
25
26		DNA : read2.p1k
27		CG
28		ACGTT
29
30		BaseQuality : read2.p1k
31		9 9 40 41 42 42 4
32
33		Sequence : read2.p1k
34		Is_read
35		SCF_File read2.p1kSCF
36		Template read2
37		Insert_size 2000 4000
38		Ligation_no 23456
39		Primer Universal_primer
40		Strand Forward
41		Dye Dye_terminator
42		Clone clone2
43		Seq_vec SVEC 1 32 puc19
44		Sequencing_vector "puc19"
45		ProcessStatus PASS
46		Unpadded
47		Align_to_SCF 1 1347 1 1347

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~~pyfastaq/tests/data/caf_test.to_fastq.no_trim.min_length_0.fq~~ less more

0		@read1.p1k
1		NACGTAN
2		+
3		%9KLI?)
4		@read2.p1k
5		CGACGTT
6		+
7		**IJKK%

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~~pyfastaq/tests/data/caf_test.to_fastq.trim.min_length_6.fq~~ less more

0		@read2.p1k
1		CGACGTT
2		+
3		**IJKK%

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~~pyfastaq/tests/data/readnames_with_comments.fastq~~ less more

0		@A1234::15950:1663 stuff_to_remove
1		TCGTAAGCCTGCTCGAGC
2		+
3		>>3>>44@CFFFGG??EE
4		@A1234::16080:1672 stuff_to_remove
5		CCATCGTCTTCGCCCTGC
6		+
7		111AA1AAAAF1EAEGAG
8		@A1234::12967:1677 stuff_to_remove
9		CTCCAGCATCGTGCAAAT
10		+
11		3>>A?@CBDFAAACCBAF
12		@A1234::16114:1681 stuff_to_remove
13		TTGATATAGAGATACTTC
14		+
15		3>A3A5D55DBFFDFGGG
16		@A1234::16669:1683 stuff_to_remove
17		CTGCGCGACTATACGCAG
18		+
19		1>1>>>A1>D?FF10E0A⏎

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~~pyfastaq/tests/data/readnames_with_comments.fastq.filtered~~ less more

0		@A1234::12967:1677 stuff_to_remove
1		CTCCAGCATCGTGCAAAT
2		+
3		3>>A?@CBDFAAACCBAF

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~~pyfastaq/tests/data/readnames_with_comments.fastq.ids~~ less more

0

A1234::12967:1677⏎

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~~pyfastaq/tests/data/sequences_test.embl~~ less more

0		ID seq1; SV 1; linear; mRNA; STD; PLN; 1859 BP.
1		XX
2		AC X56734; S46826;
3		XX
4		DT 12-SEP-1991 (Rel. 29, Created)
5		DT 25-NOV-2005 (Rel. 85, Last updated, Version 11)
6		XX
7		DE Trifolium repens mRNA for non-cyanogenic beta-glucosidase
8		XX
9		KW beta-glucosidase.
10		XX
11		OS Trifolium repens (white clover)
12		OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
13		OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
14		OC fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium.
15		XX
16		RN [5]
17		RP 1-1859
18		RX DOI; 10.1007/BF00039495.
19		RX PUBMED; 1907511.
20		RA Oxtoby E., Dunn M.A., Pancoro A., Hughes M.A.;
21		RT "Nucleotide and derived amino acid sequence of the cyanogenic
22		RT beta-glucosidase (linamarase) from white clover (Trifolium repens L.)";
23		RL Plant Mol. Biol. 17(2):209-219(1991).
24		XX
25		RN [6]
26		RP 1-1859
27		RA Hughes M.A.;
28		RT ;
29		RL Submitted (19-NOV-1990) to the INSDC.
30		RL Hughes M.A., University of Newcastle Upon Tyne, Medical School, Newcastle
31		RL Upon Tyne, NE2 4HH, UK
32		XX
33		DR EuropePMC; PMC99098; 11752244.
34		XX
35		FH Key Location/Qualifiers
36		FH
37		FT source 1..1859
38		FT /organism="Trifolium repens"
39		FT /mol_type="mRNA"
40		FT /clone_lib="lambda gt10"
41		FT /clone="TRE361"
42		FT /tissue_type="leaves"
43		FT /db_xref="taxon:3899"
44		FT mRNA 1..1859
45		FT /experiment="experimental evidence, no additional details
46		FT recorded"
47		FT CDS 14..1495
48		FT /product="beta-glucosidase"
49		FT /EC_number="3.2.1.21"
50		FT /note="non-cyanogenic"
51		FT /db_xref="GOA:P26204"
52		FT /db_xref="InterPro:IPR001360"
53		FT /db_xref="InterPro:IPR013781"
54		FT /db_xref="InterPro:IPR017853"
55		FT /db_xref="InterPro:IPR018120"
56		FT /db_xref="UniProtKB/Swiss-Prot:P26204"
57		FT /protein_id="CAA40058.1"
58		FT /translation="MDFIVAIFALFVISSFTITSTNAVEASTLLDIGNLSRSSFPRGFI
59		FT FGAGSSAYQFEGAVNEGGRGPSIWDTFTHKYPEKIRDGSNADITVDQYHRYKEDVGIMK
60		FT DQNMDSYRFSISWPRILPKGKLSGGINHEGIKYYNNLINELLANGIQPFVTLFHWDLPQ
61		FT VLEDEYGGFLNSGVINDFRDYTDLCFKEFGDRVRYWSTLNEPWVFSNSGYALGTNAPGR
62		FT CSASNVAKPGDSGTGPYIVTHNQILAHAEAVHVYKTKYQAYQKGKIGITLVSNWLMPLD
63		FT DNSIPDIKAAERSLDFQFGLFMEQLTTGDYSKSMRRIVKNRLPKFSKFESSLVNGSFDF
64		FT IGINYYSSSYISNAPSHGNAKPSYSTNPMTNISFEKHGIPLGPRAASIWIYVYPYMFIQ
65		FT EDFEIFCYILKINITILQFSITENGMNEFNDATLPVEEALLNTYRIDYYYRHLYYIRSA
66		FT IRAGSNVKGFYAWSFLDCNEWFAGFTVRFGLNFVD"
67		XX
68		SQ Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other;
69		aaacaaacca aatatggatt ttattgtagc catatttgct ctgtttgtta ttagctcatt 60
70		cacaattact tccacaaatg cagttgaagc ttctactctt cttgacatag gtaacctgag 120
71		tcggagcagt tttcctcgtg gcttcatctt tggtgctgga tcttcagcat accaatttga 180
72		aggtgcagta aacgaaggcg gtagaggacc aagtatttgg gataccttca cccataaata 240
73		tccagaaaaa ataagggatg gaagcaatgc agacatcacg gttgaccaat atcaccgcta 300
74		caaggaagat gttgggatta tgaaggatca aaatatggat tcgtatagat tctcaatctc 360
75		ttggccaaga atactcccaa agggaaagtt gagcggaggc ataaatcacg aaggaatcaa 420
76		atattacaac aaccttatca acgaactatt ggctaacggt atacaaccat ttgtaactct 480
77		ttttcattgg gatcttcccc aagtcttaga agatgagtat ggtggtttct taaactccgg 540
78		tgtaataaat gattttcgag actatacgga tctttgcttc aaggaatttg gagatagagt 600
79		gaggtattgg agtactctaa atgagccatg ggtgtttagc aattctggat atgcactagg 660
80		aacaaatgca ccaggtcgat gttcggcctc caacgtggcc aagcctggtg attctggaac 720
81		aggaccttat atagttacac acaatcaaat tcttgctcat gcagaagctg tacatgtgta 780
82		taagactaaa taccaggcat atcaaaaggg aaagataggc ataacgttgg tatctaactg 840
83		gttaatgcca cttgatgata atagcatacc agatataaag gctgccgaga gatcacttga 900
84		cttccaattt ggattgttta tggaacaatt aacaacagga gattattcta agagcatgcg 960
85		gcgtatagtt aaaaaccgat tacctaagtt ctcaaaattc gaatcaagcc tagtgaatgg 1020
86		ttcatttgat tttattggta taaactatta ctcttctagt tatattagca atgccccttc 1080
87		acatggcaat gccaaaccca gttactcaac aaatcctatg accaatattt catttgaaaa 1140
88		acatgggata cccttaggtc caagggctgc ttcaatttgg atatatgttt atccatatat 1200
89		gtttatccaa gaggacttcg agatcttttg ttacatatta aaaataaata taacaatcct 1260
90		gcaattttca atcactgaaa atggtatgaa tgaattcaac gatgcaacac ttccagtaga 1320
91		agaagctctt ttgaatactt acagaattga ttactattac cgtcacttat actacattcg 1380
92		ttctgcaatc agggctggct caaatgtgaa gggtttttac gcatggtcat ttttggactg 1440
93		taatgaatgg tttgcaggct ttactgttcg ttttggatta aactttgtag attagaaaga 1500
94		tggattaaaa aggtacccta agctttctgc ccaatggtac aagaactttc tcaaaagaaa 1560
95		ctagctagta ttattaaaag aactttgtag tagattacag tacatcgttt gaagttgagt 1620
96		tggtgcacct aattaaataa aagaggttac tcttaacata tttttaggcc attcgttgtg 1680
97		aagttgttag gctgttattt ctattatact atgttgtagt aataagtgca ttgttgtacc 1740
98		agaagctatg atcataacta taggttgatc cttcatgtat cagtttgatg ttgagaatac 1800
99		tttgaattaa aagtcttttt ttattttttt aaaaaaaaaa aaaaaaaaaa aaaaaaaaa 1859
100		//
101		ID seq2; SV 1; linear; mRNA; STD; PLN; 1859 BP.
102		XX
103		AC X56734; S46826;
104		XX
105		DT 12-SEP-1991 (Rel. 29, Created)
106		DT 25-NOV-2005 (Rel. 85, Last updated, Version 11)
107		XX
108		DE Trifolium repens mRNA for non-cyanogenic beta-glucosidase
109		XX
110		KW beta-glucosidase.
111		XX
112		OS Trifolium repens (white clover)
113		OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
114		OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
115		OC fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium.
116		XX
117		RN [5]
118		RP 1-1859
119		RX DOI; 10.1007/BF00039495.
120		RX PUBMED; 1907511.
121		RA Oxtoby E., Dunn M.A., Pancoro A., Hughes M.A.;
122		RT "Nucleotide and derived amino acid sequence of the cyanogenic
123		RT beta-glucosidase (linamarase) from white clover (Trifolium repens L.)";
124		RL Plant Mol. Biol. 17(2):209-219(1991).
125		XX
126		RN [6]
127		RP 1-1859
128		RA Hughes M.A.;
129		RT ;
130		RL Submitted (19-NOV-1990) to the INSDC.
131		RL Hughes M.A., University of Newcastle Upon Tyne, Medical School, Newcastle
132		RL Upon Tyne, NE2 4HH, UK
133		XX
134		DR EuropePMC; PMC99098; 11752244.
135		XX
136		FH Key Location/Qualifiers
137		FH
138		FT source 1..1859
139		FT /organism="Trifolium repens"
140		FT /mol_type="mRNA"
141		FT /clone_lib="lambda gt10"
142		FT /clone="TRE361"
143		FT /tissue_type="leaves"
144		FT /db_xref="taxon:3899"
145		FT mRNA 1..1859
146		FT /experiment="experimental evidence, no additional details
147		FT recorded"
148		FT CDS 14..1495
149		FT /product="beta-glucosidase"
150		FT /EC_number="3.2.1.21"
151		FT /note="non-cyanogenic"
152		FT /db_xref="GOA:P26204"
153		FT /db_xref="InterPro:IPR001360"
154		FT /db_xref="InterPro:IPR013781"
155		FT /db_xref="InterPro:IPR017853"
156		FT /db_xref="InterPro:IPR018120"
157		FT /db_xref="UniProtKB/Swiss-Prot:P26204"
158		FT /protein_id="CAA40058.1"
159		FT /translation="MDFIVAIFALFVISSFTITSTNAVEASTLLDIGNLSRSSFPRGFI
160		FT FGAGSSAYQFEGAVNEGGRGPSIWDTFTHKYPEKIRDGSNADITVDQYHRYKEDVGIMK
161		FT DQNMDSYRFSISWPRILPKGKLSGGINHEGIKYYNNLINELLANGIQPFVTLFHWDLPQ
162		FT VLEDEYGGFLNSGVINDFRDYTDLCFKEFGDRVRYWSTLNEPWVFSNSGYALGTNAPGR
163		FT CSASNVAKPGDSGTGPYIVTHNQILAHAEAVHVYKTKYQAYQKGKIGITLVSNWLMPLD
164		FT DNSIPDIKAAERSLDFQFGLFMEQLTTGDYSKSMRRIVKNRLPKFSKFESSLVNGSFDF
165		FT IGINYYSSSYISNAPSHGNAKPSYSTNPMTNISFEKHGIPLGPRAASIWIYVYPYMFIQ
166		FT EDFEIFCYILKINITILQFSITENGMNEFNDATLPVEEALLNTYRIDYYYRHLYYIRSA
167		FT IRAGSNVKGFYAWSFLDCNEWFAGFTVRFGLNFVD"
168		XX
169		SQ Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other;
170		aaacaaacca aatatggatt ttattgtagc catatttgct ctgtttgtta ttagctcatt 60
171		cacaattact tccacaaatg cagttgaagc ttctactctt cttgacatag gtaacctgag 120
172		tcggagcagt tttcctcgtg gcttcatctt tggtgctgga tcttcagcat accaatttga 180
173		aggtgcagta aacgaaggcg gtagaggacc aagtatttgg gataccttca cccataaata 240
174		tccagaaaaa ataagggatg gaagcaatgc agacatcacg gttgaccaat atcaccgcta 300
175		caaggaagat gttgggatta tgaaggatca aaatatggat tcgtatagat tctcaatctc 360
176		ttggccaaga atactcccaa agggaaagtt gagcggaggc ataaatcacg aaggaatcaa 420
177		atattacaac aaccttatca acgaactatt ggctaacggt atacaaccat ttgtaactct 480
178		ttttcattgg gatcttcccc aagtcttaga agatgagtat ggtggtttct taaactccgg 540
179		tgtaataaat gattttcgag actatacgga tctttgcttc aaggaatttg gagatagagt 600
180		gaggtattgg agtactctaa atgagccatg ggtgtttagc aattctggat atgcactagg 660
181		aacaaatgca ccaggtcgat gttcggcctc caacgtggcc aagcctggtg attctggaac 720
182		aggaccttat atagttacac acaatcaaat tcttgctcat gcagaagctg tacatgtgta 780
183		taagactaaa taccaggcat atcaaaaggg aaagataggc ataacgttgg tatctaactg 840
184		gttaatgcca cttgatgata atagcatacc agatataaag gctgccgaga gatcacttga 900
185		cttccaattt ggattgttta tggaacaatt aacaacagga gattattcta agagcatgcg 960
186		gcgtatagtt aaaaaccgat tacctaagtt ctcaaaattc gaatcaagcc tagtgaatgg 1020
187		ttcatttgat tttattggta taaactatta ctcttctagt tatattagca atgccccttc 1080
188		acatggcaat gccaaaccca gttactcaac aaatcctatg accaatattt catttgaaaa 1140
189		acatgggata cccttaggtc caagggctgc ttcaatttgg atatatgttt atccatatat 1200
190		gtttatccaa gaggacttcg agatcttttg ttacatatta aaaataaata taacaatcct 1260
191		gcaattttca atcactgaaa atggtatgaa tgaattcaac gatgcaacac ttccagtaga 1320
192		agaagctctt ttgaatactt acagaattga ttactattac cgtcacttat actacattcg 1380
193		ttctgcaatc agggctggct caaatgtgaa gggtttttac gcatggtcat ttttggactg 1440
194		taatgaatgg tttgcaggct ttactgttcg ttttggatta aactttgtag attagaaaga 1500
195		tggattaaaa aggtacccta agctttctgc ccaatggtac aagaactttc tcaaaagaaa 1560
196		ctagctagta ttattaaaag aactttgtag tagattacag tacatcgttt gaagttgagt 1620
197		tggtgcacct aattaaataa aagaggttac tcttaacata tttttaggcc attcgttgtg 1680
198		aagttgttag gctgttattt ctattatact atgttgtagt aataagtgca ttgttgtacc 1740
199		agaagctatg atcataacta taggttgatc cttcatgtat cagtttgatg ttgagaatac 1800
200		tttgaattaa aagtcttttt ttattttttt aaaaaaaaaa aaaaaaaaaa ccccccccc 1859
201		//
202

+0

-202

~~pyfastaq/tests/data/sequences_test.embl.bad~~ less more

0		ID seq1; SV 1; linear; mRNA; STD; PLN; 1859 BP.
1		XX
2		AC X56734; S46826;
3		XX
4		DT 12-SEP-1991 (Rel. 29, Created)
5		DT 25-NOV-2005 (Rel. 85, Last updated, Version 11)
6		XX
7		DE Trifolium repens mRNA for non-cyanogenic beta-glucosidase
8		XX
9		KW beta-glucosidase.
10		XX
11		OS Trifolium repens (white clover)
12		OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
13		OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
14		OC fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium.
15		XX
16		RN [5]
17		RP 1-1859
18		RX DOI; 10.1007/BF00039495.
19		RX PUBMED; 1907511.
20		RA Oxtoby E., Dunn M.A., Pancoro A., Hughes M.A.;
21		RT "Nucleotide and derived amino acid sequence of the cyanogenic
22		RT beta-glucosidase (linamarase) from white clover (Trifolium repens L.)";
23		RL Plant Mol. Biol. 17(2):209-219(1991).
24		XX
25		RN [6]
26		RP 1-1859
27		RA Hughes M.A.;
28		RT ;
29		RL Submitted (19-NOV-1990) to the INSDC.
30		RL Hughes M.A., University of Newcastle Upon Tyne, Medical School, Newcastle
31		RL Upon Tyne, NE2 4HH, UK
32		XX
33		DR EuropePMC; PMC99098; 11752244.
34		XX
35		FH Key Location/Qualifiers
36		FH
37		FT source 1..1859
38		FT /organism="Trifolium repens"
39		FT /mol_type="mRNA"
40		FT /clone_lib="lambda gt10"
41		FT /clone="TRE361"
42		FT /tissue_type="leaves"
43		FT /db_xref="taxon:3899"
44		FT mRNA 1..1859
45		FT /experiment="experimental evidence, no additional details
46		FT recorded"
47		FT CDS 14..1495
48		FT /product="beta-glucosidase"
49		FT /EC_number="3.2.1.21"
50		FT /note="non-cyanogenic"
51		FT /db_xref="GOA:P26204"
52		FT /db_xref="InterPro:IPR001360"
53		FT /db_xref="InterPro:IPR013781"
54		FT /db_xref="InterPro:IPR017853"
55		FT /db_xref="InterPro:IPR018120"
56		FT /db_xref="UniProtKB/Swiss-Prot:P26204"
57		FT /protein_id="CAA40058.1"
58		FT /translation="MDFIVAIFALFVISSFTITSTNAVEASTLLDIGNLSRSSFPRGFI
59		FT FGAGSSAYQFEGAVNEGGRGPSIWDTFTHKYPEKIRDGSNADITVDQYHRYKEDVGIMK
60		FT DQNMDSYRFSISWPRILPKGKLSGGINHEGIKYYNNLINELLANGIQPFVTLFHWDLPQ
61		FT VLEDEYGGFLNSGVINDFRDYTDLCFKEFGDRVRYWSTLNEPWVFSNSGYALGTNAPGR
62		FT CSASNVAKPGDSGTGPYIVTHNQILAHAEAVHVYKTKYQAYQKGKIGITLVSNWLMPLD
63		FT DNSIPDIKAAERSLDFQFGLFMEQLTTGDYSKSMRRIVKNRLPKFSKFESSLVNGSFDF
64		FT IGINYYSSSYISNAPSHGNAKPSYSTNPMTNISFEKHGIPLGPRAASIWIYVYPYMFIQ
65		FT EDFEIFCYILKINITILQFSITENGMNEFNDATLPVEEALLNTYRIDYYYRHLYYIRSA
66		FT IRAGSNVKGFYAWSFLDCNEWFAGFTVRFGLNFVD"
67		XX
68		SQ Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other;
69		aaacaaacca aatatggatt ttattgtagc catatttgct ctgtttgtta ttagctcatt 60
70		cacaattact tccacaaatg cagttgaagc ttctactctt cttgacatag gtaacctgag 120
71		tcggagcagt tttcctcgtg gcttcatctt tggtgctgga tcttcagcat accaatttga 180
72		aggtgcagta aacgaaggcg gtagaggacc aagtatttgg gataccttca cccataaata 240
73		tccagaaaaa ataagggatg gaagcaatgc agacatcacg gttgaccaat atcaccgcta 300
74		caaggaagat gttgggatta tgaaggatca aaatatggat tcgtatagat tctcaatctc 360
75		ttggccaaga atactcccaa agggaaagtt gagcggaggc ataaatcacg aaggaatcaa 420
76		atattacaac aaccttatca acgaactatt ggctaacggt atacaaccat ttgtaactct 480
77		ttttcattgg gatcttcccc aagtcttaga agatgagtat ggtggtttct taaactccgg 540
78		tgtaataaat gattttcgag actatacgga tctttgcttc aaggaatttg gagatagagt 600
79		gaggtattgg agtactctaa atgagccatg ggtgtttagc aattctggat atgcactagg 660
80		aacaaatgca ccaggtcgat gttcggcctc caacgtggcc aagcctggtg attctggaac 720
81		aggaccttat atagttacac acaatcaaat tcttgctcat gcagaagctg tacatgtgta 780
82		taagactaaa taccaggcat atcaaaaggg aaagataggc ataacgttgg tatctaactg 840
83		gttaatgcca cttgatgata atagcatacc agatataaag gctgccgaga gatcacttga 900
84		cttccaattt ggattgttta tggaacaatt aacaacagga gattattcta agagcatgcg 960
85		gcgtatagtt aaaaaccgat tacctaagtt ctcaaaattc gaatcaagcc tagtgaatgg 1020
86		ttcatttgat tttattggta taaactatta ctcttctagt tatattagca atgccccttc 1080
87		acatggcaat gccaaaccca gttactcaac aaatcctatg accaatattt catttgaaaa 1140
88		acatgggata cccttaggtc caagggctgc ttcaatttgg atatatgttt atccatatat 1200
89		gtttatccaa gaggacttcg agatcttttg ttacatatta aaaataaata taacaatcct 1260
90		gcaattttca atcactgaaa atggtatgaa tgaattcaac gatgcaacac ttccagtaga 1320
91		agaagctctt ttgaatactt acagaattga ttactattac cgtcacttat actacattcg 1380
92		ttctgcaatc agggctggct caaatgtgaa gggtttttac gcatggtcat ttttggactg 1440
93		taatgaatgg tttgcaggct ttactgttcg ttttggatta aactttgtag attagaaaga 1500
94		tggattaaaa aggtacccta agctttctgc ccaatggtac aagaactttc tcaaaagaaa 1560
95		ctagctagta ttattaaaag aactttgtag tagattacag tacatcgttt gaagttgagt 1620
96		tggtgcacct aattaaataa aagaggttac tcttaacata tttttaggcc attcgttgtg 1680
97		aagttgttag gctgttattt ctattatact atgttgtagt aataagtgca ttgttgtacc 1740
98		agaagctatg atcataacta taggttgatc cttcatgtat cagtttgatg ttgagaatac 1800
99		tttgaattaa aagtcttttt ttattttttt aaaaaaaaaa aaaaaaaaaa aaaaaaaaa 1859
100		//
101		ID seq2; SV 1; linear; mRNA; STD; PLN; 1859 BP.
102		XX
103		AC X56734; S46826;
104		XX
105		DT 12-SEP-1991 (Rel. 29, Created)
106		DT 25-NOV-2005 (Rel. 85, Last updated, Version 11)
107		XX
108		DE Trifolium repens mRNA for non-cyanogenic beta-glucosidase
109		XX
110		KW beta-glucosidase.
111		XX
112		OS Trifolium repens (white clover)
113		OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
114		OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
115		OC fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium.
116		XX
117		RN [5]
118		RP 1-1859
119		RX DOI; 10.1007/BF00039495.
120		RX PUBMED; 1907511.
121		RA Oxtoby E., Dunn M.A., Pancoro A., Hughes M.A.;
122		RT "Nucleotide and derived amino acid sequence of the cyanogenic
123		RT beta-glucosidase (linamarase) from white clover (Trifolium repens L.)";
124		RL Plant Mol. Biol. 17(2):209-219(1991).
125		XX
126		RN [6]
127		RP 1-1859
128		RA Hughes M.A.;
129		RT ;
130		RL Submitted (19-NOV-1990) to the INSDC.
131		RL Hughes M.A., University of Newcastle Upon Tyne, Medical School, Newcastle
132		RL Upon Tyne, NE2 4HH, UK
133		XX
134		DR EuropePMC; PMC99098; 11752244.
135		XX
136		FH Key Location/Qualifiers
137		FH
138		FT source 1..1859
139		FT /organism="Trifolium repens"
140		FT /mol_type="mRNA"
141		FT /clone_lib="lambda gt10"
142		FT /clone="TRE361"
143		FT /tissue_type="leaves"
144		FT /db_xref="taxon:3899"
145		FT mRNA 1..1859
146		FT /experiment="experimental evidence, no additional details
147		FT recorded"
148		FT CDS 14..1495
149		FT /product="beta-glucosidase"
150		FT /EC_number="3.2.1.21"
151		FT /note="non-cyanogenic"
152		FT /db_xref="GOA:P26204"
153		FT /db_xref="InterPro:IPR001360"
154		FT /db_xref="InterPro:IPR013781"
155		FT /db_xref="InterPro:IPR017853"
156		FT /db_xref="InterPro:IPR018120"
157		FT /db_xref="UniProtKB/Swiss-Prot:P26204"
158		FT /protein_id="CAA40058.1"
159		FT /translation="MDFIVAIFALFVISSFTITSTNAVEASTLLDIGNLSRSSFPRGFI
160		FT FGAGSSAYQFEGAVNEGGRGPSIWDTFTHKYPEKIRDGSNADITVDQYHRYKEDVGIMK
161		FT DQNMDSYRFSISWPRILPKGKLSGGINHEGIKYYNNLINELLANGIQPFVTLFHWDLPQ
162		FT VLEDEYGGFLNSGVINDFRDYTDLCFKEFGDRVRYWSTLNEPWVFSNSGYALGTNAPGR
163		FT CSASNVAKPGDSGTGPYIVTHNQILAHAEAVHVYKTKYQAYQKGKIGITLVSNWLMPLD
164		FT DNSIPDIKAAERSLDFQFGLFMEQLTTGDYSKSMRRIVKNRLPKFSKFESSLVNGSFDF
165		FT IGINYYSSSYISNAPSHGNAKPSYSTNPMTNISFEKHGIPLGPRAASIWIYVYPYMFIQ
166		FT EDFEIFCYILKINITILQFSITENGMNEFNDATLPVEEALLNTYRIDYYYRHLYYIRSA
167		FT IRAGSNVKGFYAWSFLDCNEWFAGFTVRFGLNFVD"
168		XX
169		aaacaaacca aatatggatt ttattgtagc catatttgct ctgtttgtta ttagctcatt 60
170		cacaattact tccacaaatg cagttgaagc ttctactctt cttgacatag gtaacctgag 120
171		tcggagcagt tttcctcgtg gcttcatctt tggtgctgga tcttcagcat accaatttga 180
172		aggtgcagta aacgaaggcg gtagaggacc aagtatttgg gataccttca cccataaata 240
173		tccagaaaaa ataagggatg gaagcaatgc agacatcacg gttgaccaat atcaccgcta 300
174		caaggaagat gttgggatta tgaaggatca aaatatggat tcgtatagat tctcaatctc 360
175		ttggccaaga atactcccaa agggaaagtt gagcggaggc ataaatcacg aaggaatcaa 420
176		atattacaac aaccttatca acgaactatt ggctaacggt atacaaccat ttgtaactct 480
177		ttttcattgg gatcttcccc aagtcttaga agatgagtat ggtggtttct taaactccgg 540
178		tgtaataaat gattttcgag actatacgga tctttgcttc aaggaatttg gagatagagt 600
179		gaggtattgg agtactctaa atgagccatg ggtgtttagc aattctggat atgcactagg 660
180		aacaaatgca ccaggtcgat gttcggcctc caacgtggcc aagcctggtg attctggaac 720
181		aggaccttat atagttacac acaatcaaat tcttgctcat gcagaagctg tacatgtgta 780
182		taagactaaa taccaggcat atcaaaaggg aaagataggc ataacgttgg tatctaactg 840
183		gttaatgcca cttgatgata atagcatacc agatataaag gctgccgaga gatcacttga 900
184		cttccaattt ggattgttta tggaacaatt aacaacagga gattattcta agagcatgcg 960
185		gcgtatagtt aaaaaccgat tacctaagtt ctcaaaattc gaatcaagcc tagtgaatgg 1020
186		ttcatttgat tttattggta taaactatta ctcttctagt tatattagca atgccccttc 1080
187		acatggcaat gccaaaccca gttactcaac aaatcctatg accaatattt catttgaaaa 1140
188		acatgggata cccttaggtc caagggctgc ttcaatttgg atatatgttt atccatatat 1200
189		gtttatccaa gaggacttcg agatcttttg ttacatatta aaaataaata taacaatcct 1260
190		gcaattttca atcactgaaa atggtatgaa tgaattcaac gatgcaacac ttccagtaga 1320
191		agaagctctt ttgaatactt acagaattga ttactattac cgtcacttat actacattcg 1380
192		ttctgcaatc agggctggct caaatgtgaa gggtttttac gcatggtcat ttttggactg 1440
193		taatgaatgg tttgcaggct ttactgttcg ttttggatta aactttgtag attagaaaga 1500
194		tggattaaaa aggtacccta agctttctgc ccaatggtac aagaactttc tcaaaagaaa 1560
195		ctagctagta ttattaaaag aactttgtag tagattacag tacatcgttt gaagttgagt 1620
196		tggtgcacct aattaaataa aagaggttac tcttaacata tttttaggcc attcgttgtg 1680
197		aagttgttag gctgttattt ctattatact atgttgtagt aataagtgca ttgttgtacc 1740
198		agaagctatg atcataacta taggttgatc cttcatgtat cagtttgatg ttgagaatac 1800
199		tttgaattaa aagtcttttt ttattttttt aaaaaaaaaa aaaaaaaaaa ccccccccc 1859
200		//
201

+0

-202

~~pyfastaq/tests/data/sequences_test.embl.bad2~~ less more

0		ID seq1; SV 1; linear; mRNA; STD; PLN; 1859 BP.
1		XX
2		AC X56734; S46826;
3		XX
4		DT 12-SEP-1991 (Rel. 29, Created)
5		DT 25-NOV-2005 (Rel. 85, Last updated, Version 11)
6		XX
7		DE Trifolium repens mRNA for non-cyanogenic beta-glucosidase
8		XX
9		KW beta-glucosidase.
10		XX
11		OS Trifolium repens (white clover)
12		OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
13		OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
14		OC fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium.
15		XX
16		RN [5]
17		RP 1-1859
18		RX DOI; 10.1007/BF00039495.
19		RX PUBMED; 1907511.
20		RA Oxtoby E., Dunn M.A., Pancoro A., Hughes M.A.;
21		RT "Nucleotide and derived amino acid sequence of the cyanogenic
22		RT beta-glucosidase (linamarase) from white clover (Trifolium repens L.)";
23		RL Plant Mol. Biol. 17(2):209-219(1991).
24		XX
25		RN [6]
26		RP 1-1859
27		RA Hughes M.A.;
28		RT ;
29		RL Submitted (19-NOV-1990) to the INSDC.
30		RL Hughes M.A., University of Newcastle Upon Tyne, Medical School, Newcastle
31		RL Upon Tyne, NE2 4HH, UK
32		XX
33		DR EuropePMC; PMC99098; 11752244.
34		XX
35		FH Key Location/Qualifiers
36		FH
37		FT source 1..1859
38		FT /organism="Trifolium repens"
39		FT /mol_type="mRNA"
40		FT /clone_lib="lambda gt10"
41		FT /clone="TRE361"
42		FT /tissue_type="leaves"
43		FT /db_xref="taxon:3899"
44		FT mRNA 1..1859
45		FT /experiment="experimental evidence, no additional details
46		FT recorded"
47		FT CDS 14..1495
48		FT /product="beta-glucosidase"
49		FT /EC_number="3.2.1.21"
50		FT /note="non-cyanogenic"
51		FT /db_xref="GOA:P26204"
52		FT /db_xref="InterPro:IPR001360"
53		FT /db_xref="InterPro:IPR013781"
54		FT /db_xref="InterPro:IPR017853"
55		FT /db_xref="InterPro:IPR018120"
56		FT /db_xref="UniProtKB/Swiss-Prot:P26204"
57		FT /protein_id="CAA40058.1"
58		FT /translation="MDFIVAIFALFVISSFTITSTNAVEASTLLDIGNLSRSSFPRGFI
59		FT FGAGSSAYQFEGAVNEGGRGPSIWDTFTHKYPEKIRDGSNADITVDQYHRYKEDVGIMK
60		FT DQNMDSYRFSISWPRILPKGKLSGGINHEGIKYYNNLINELLANGIQPFVTLFHWDLPQ
61		FT VLEDEYGGFLNSGVINDFRDYTDLCFKEFGDRVRYWSTLNEPWVFSNSGYALGTNAPGR
62		FT CSASNVAKPGDSGTGPYIVTHNQILAHAEAVHVYKTKYQAYQKGKIGITLVSNWLMPLD
63		FT DNSIPDIKAAERSLDFQFGLFMEQLTTGDYSKSMRRIVKNRLPKFSKFESSLVNGSFDF
64		FT IGINYYSSSYISNAPSHGNAKPSYSTNPMTNISFEKHGIPLGPRAASIWIYVYPYMFIQ
65		FT EDFEIFCYILKINITILQFSITENGMNEFNDATLPVEEALLNTYRIDYYYRHLYYIRSA
66		FT IRAGSNVKGFYAWSFLDCNEWFAGFTVRFGLNFVD"
67		XX
68		SQ Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other;
69		aaacaaacca aatatggatt ttattgtagc catatttgct ctgtttgtta ttagctcatt 60
70		cacaattact tccacaaatg cagttgaagc ttctactctt cttgacatag gtaacctgag 120
71		tcggagcagt tttcctcgtg gcttcatctt tggtgctgga tcttcagcat accaatttga 180
72		aggtgcagta aacgaaggcg gtagaggacc aagtatttgg gataccttca cccataaata 240
73		tccagaaaaa ataagggatg gaagcaatgc agacatcacg gttgaccaat atcaccgcta 300
74		caaggaagat gttgggatta tgaaggatca aaatatggat tcgtatagat tctcaatctc 360
75		ttggccaaga atactcccaa agggaaagtt gagcggaggc ataaatcacg aaggaatcaa 420
76		atattacaac aaccttatca acgaactatt ggctaacggt atacaaccat ttgtaactct 480
77		ttttcattgg gatcttcccc aagtcttaga agatgagtat ggtggtttct taaactccgg 540
78		tgtaataaat gattttcgag actatacgga tctttgcttc aaggaatttg gagatagagt 600
79		gaggtattgg agtactctaa atgagccatg ggtgtttagc aattctggat atgcactagg 660
80		aacaaatgca ccaggtcgat gttcggcctc caacgtggcc aagcctggtg attctggaac 720
81		aggaccttat atagttacac acaatcaaat tcttgctcat gcagaagctg tacatgtgta 780
82		taagactaaa taccaggcat atcaaaaggg aaagataggc ataacgttgg tatctaactg 840
83		gttaatgcca cttgatgata atagcatacc agatataaag gctgccgaga gatcacttga 900
84		cttccaattt ggattgttta tggaacaatt aacaacagga gattattcta agagcatgcg 960
85		gcgtatagtt aaaaaccgat tacctaagtt ctcaaaattc gaatcaagcc tagtgaatgg 1020
86		ttcatttgat tttattggta taaactatta ctcttctagt tatattagca atgccccttc 1080
87		acatggcaat gccaaaccca gttactcaac aaatcctatg accaatattt catttgaaaa 1140
88		acatgggata cccttaggtc caagggctgc ttcaatttgg atatatgttt atccatatat 1200
89		gtttatccaa gaggacttcg agatcttttg ttacatatta aaaataaata taacaatcct 1260
90		gcaattttca atcactgaaa atggtatgaa tgaattcaac gatgcaacac ttccagtaga 1320
91		agaagctctt ttgaatactt acagaattga ttactattac cgtcacttat actacattcg 1380
92		ttctgcaatc agggctggct caaatgtgaa gggtttttac gcatggtcat ttttggactg 1440
93		taatgaatgg tttgcaggct ttactgttcg ttttggatta aactttgtag attagaaaga 1500
94		tggattaaaa aggtacccta agctttctgc ccaatggtac aagaactttc tcaaaagaaa 1560
95		ctagctagta ttattaaaag aactttgtag tagattacag tacatcgttt gaagttgagt 1620
96		tggtgcacct aattaaataa aagaggttac tcttaacata tttttaggcc attcgttgtg 1680
97		aagttgttag gctgttattt ctattatact atgttgtagt aataagtgca ttgttgtacc 1740
98		agaagctatg atcataacta taggttgatc cttcatgtat cagtttgatg ttgagaatac 1800
99		tttgaattaa aagtcttttt ttattttttt aaaaaaaaaa aaaaaaaaaa aaaaaaaaa 1859
100		ID seq2; SV 1; linear; mRNA; STD; PLN; 1859 BP.
101		XX
102		AC X56734; S46826;
103		XX
104		DT 12-SEP-1991 (Rel. 29, Created)
105		DT 25-NOV-2005 (Rel. 85, Last updated, Version 11)
106		XX
107		DE Trifolium repens mRNA for non-cyanogenic beta-glucosidase
108		XX
109		KW beta-glucosidase.
110		XX
111		OS Trifolium repens (white clover)
112		OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
113		OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
114		OC fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium.
115		XX
116		RN [5]
117		RP 1-1859
118		RX DOI; 10.1007/BF00039495.
119		RX PUBMED; 1907511.
120		RA Oxtoby E., Dunn M.A., Pancoro A., Hughes M.A.;
121		RT "Nucleotide and derived amino acid sequence of the cyanogenic
122		RT beta-glucosidase (linamarase) from white clover (Trifolium repens L.)";
123		RL Plant Mol. Biol. 17(2):209-219(1991).
124		XX
125		RN [6]
126		RP 1-1859
127		RA Hughes M.A.;
128		RT ;
129		RL Submitted (19-NOV-1990) to the INSDC.
130		RL Hughes M.A., University of Newcastle Upon Tyne, Medical School, Newcastle
131		RL Upon Tyne, NE2 4HH, UK
132		XX
133		DR EuropePMC; PMC99098; 11752244.
134		XX
135		FH Key Location/Qualifiers
136		FH
137		FT source 1..1859
138		FT /organism="Trifolium repens"
139		FT /mol_type="mRNA"
140		FT /clone_lib="lambda gt10"
141		FT /clone="TRE361"
142		FT /tissue_type="leaves"
143		FT /db_xref="taxon:3899"
144		FT mRNA 1..1859
145		FT /experiment="experimental evidence, no additional details
146		FT recorded"
147		FT CDS 14..1495
148		FT /product="beta-glucosidase"
149		FT /EC_number="3.2.1.21"
150		FT /note="non-cyanogenic"
151		FT /db_xref="GOA:P26204"
152		FT /db_xref="InterPro:IPR001360"
153		FT /db_xref="InterPro:IPR013781"
154		FT /db_xref="InterPro:IPR017853"
155		FT /db_xref="InterPro:IPR018120"
156		FT /db_xref="UniProtKB/Swiss-Prot:P26204"
157		FT /protein_id="CAA40058.1"
158		FT /translation="MDFIVAIFALFVISSFTITSTNAVEASTLLDIGNLSRSSFPRGFI
159		FT FGAGSSAYQFEGAVNEGGRGPSIWDTFTHKYPEKIRDGSNADITVDQYHRYKEDVGIMK
160		FT DQNMDSYRFSISWPRILPKGKLSGGINHEGIKYYNNLINELLANGIQPFVTLFHWDLPQ
161		FT VLEDEYGGFLNSGVINDFRDYTDLCFKEFGDRVRYWSTLNEPWVFSNSGYALGTNAPGR
162		FT CSASNVAKPGDSGTGPYIVTHNQILAHAEAVHVYKTKYQAYQKGKIGITLVSNWLMPLD
163		FT DNSIPDIKAAERSLDFQFGLFMEQLTTGDYSKSMRRIVKNRLPKFSKFESSLVNGSFDF
164		FT IGINYYSSSYISNAPSHGNAKPSYSTNPMTNISFEKHGIPLGPRAASIWIYVYPYMFIQ
165		FT EDFEIFCYILKINITILQFSITENGMNEFNDATLPVEEALLNTYRIDYYYRHLYYIRSA
166		FT IRAGSNVKGFYAWSFLDCNEWFAGFTVRFGLNFVD"
167		XX
168		SQ Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other;
169		aaacaaacca aatatggatt ttattgtagc catatttgct ctgtttgtta ttagctcatt 60
170		cacaattact tccacaaatg cagttgaagc ttctactctt cttgacatag gtaacctgag 120
171		tcggagcagt tttcctcgtg gcttcatctt tggtgctgga tcttcagcat accaatttga 180
172		aggtgcagta aacgaaggcg gtagaggacc aagtatttgg gataccttca cccataaata 240
173		tccagaaaaa ataagggatg gaagcaatgc agacatcacg gttgaccaat atcaccgcta 300
174		caaggaagat gttgggatta tgaaggatca aaatatggat tcgtatagat tctcaatctc 360
175		ttggccaaga atactcccaa agggaaagtt gagcggaggc ataaatcacg aaggaatcaa 420
176		atattacaac aaccttatca acgaactatt ggctaacggt atacaaccat ttgtaactct 480
177		ttttcattgg gatcttcccc aagtcttaga agatgagtat ggtggtttct taaactccgg 540
178		tgtaataaat gattttcgag actatacgga tctttgcttc aaggaatttg gagatagagt 600
179		gaggtattgg agtactctaa atgagccatg ggtgtttagc aattctggat atgcactagg 660
180		aacaaatgca ccaggtcgat gttcggcctc caacgtggcc aagcctggtg attctggaac 720
181		aggaccttat atagttacac acaatcaaat tcttgctcat gcagaagctg tacatgtgta 780
182		taagactaaa taccaggcat atcaaaaggg aaagataggc ataacgttgg tatctaactg 840
183		gttaatgcca cttgatgata atagcatacc agatataaag gctgccgaga gatcacttga 900
184		cttccaattt ggattgttta tggaacaatt aacaacagga gattattcta agagcatgcg 960
185		gcgtatagtt aaaaaccgat tacctaagtt ctcaaaattc gaatcaagcc tagtgaatgg 1020
186		ttcatttgat tttattggta taaactatta ctcttctagt tatattagca atgccccttc 1080
187		acatggcaat gccaaaccca gttactcaac aaatcctatg accaatattt catttgaaaa 1140
188		acatgggata cccttaggtc caagggctgc ttcaatttgg atatatgttt atccatatat 1200
189		gtttatccaa gaggacttcg agatcttttg ttacatatta aaaataaata taacaatcct 1260
190		gcaattttca atcactgaaa atggtatgaa tgaattcaac gatgcaacac ttccagtaga 1320
191		agaagctctt ttgaatactt acagaattga ttactattac cgtcacttat actacattcg 1380
192		ttctgcaatc agggctggct caaatgtgaa gggtttttac gcatggtcat ttttggactg 1440
193		taatgaatgg tttgcaggct ttactgttcg ttttggatta aactttgtag attagaaaga 1500
194		tggattaaaa aggtacccta agctttctgc ccaatggtac aagaactttc tcaaaagaaa 1560
195		ctagctagta ttattaaaag aactttgtag tagattacag tacatcgttt gaagttgagt 1620
196		tggtgcacct aattaaataa aagaggttac tcttaacata tttttaggcc attcgttgtg 1680
197		aagttgttag gctgttattt ctattatact atgttgtagt aataagtgca ttgttgtacc 1740
198		agaagctatg atcataacta taggttgatc cttcatgtat cagtttgatg ttgagaatac 1800
199		tttgaattaa aagtcttttt ttattttttt aaaaaaaaaa aaaaaaaaaa ccccccccc 1859
200		//
201

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~~pyfastaq/tests/data/sequences_test.embl.to_fasta~~ less more

0		>seq1
1		aaacaaaccaaatatggattttattgtagccatatttgctctgtttgttattagctcatt
2		cacaattacttccacaaatgcagttgaagcttctactcttcttgacataggtaacctgag
3		tcggagcagttttcctcgtggcttcatctttggtgctggatcttcagcataccaatttga
4		aggtgcagtaaacgaaggcggtagaggaccaagtatttgggataccttcacccataaata
5		tccagaaaaaataagggatggaagcaatgcagacatcacggttgaccaatatcaccgcta
6		caaggaagatgttgggattatgaaggatcaaaatatggattcgtatagattctcaatctc
7		ttggccaagaatactcccaaagggaaagttgagcggaggcataaatcacgaaggaatcaa
8		atattacaacaaccttatcaacgaactattggctaacggtatacaaccatttgtaactct
9		ttttcattgggatcttccccaagtcttagaagatgagtatggtggtttcttaaactccgg
10		tgtaataaatgattttcgagactatacggatctttgcttcaaggaatttggagatagagt
11		gaggtattggagtactctaaatgagccatgggtgtttagcaattctggatatgcactagg
12		aacaaatgcaccaggtcgatgttcggcctccaacgtggccaagcctggtgattctggaac
13		aggaccttatatagttacacacaatcaaattcttgctcatgcagaagctgtacatgtgta
14		taagactaaataccaggcatatcaaaagggaaagataggcataacgttggtatctaactg
15		gttaatgccacttgatgataatagcataccagatataaaggctgccgagagatcacttga
16		cttccaatttggattgtttatggaacaattaacaacaggagattattctaagagcatgcg
17		gcgtatagttaaaaaccgattacctaagttctcaaaattcgaatcaagcctagtgaatgg
18		ttcatttgattttattggtataaactattactcttctagttatattagcaatgccccttc
19		acatggcaatgccaaacccagttactcaacaaatcctatgaccaatatttcatttgaaaa
20		acatgggatacccttaggtccaagggctgcttcaatttggatatatgtttatccatatat
21		gtttatccaagaggacttcgagatcttttgttacatattaaaaataaatataacaatcct
22		gcaattttcaatcactgaaaatggtatgaatgaattcaacgatgcaacacttccagtaga
23		agaagctcttttgaatacttacagaattgattactattaccgtcacttatactacattcg
24		ttctgcaatcagggctggctcaaatgtgaagggtttttacgcatggtcatttttggactg
25		taatgaatggtttgcaggctttactgttcgttttggattaaactttgtagattagaaaga
26		tggattaaaaaggtaccctaagctttctgcccaatggtacaagaactttctcaaaagaaa
27		ctagctagtattattaaaagaactttgtagtagattacagtacatcgtttgaagttgagt
28		tggtgcacctaattaaataaaagaggttactcttaacatatttttaggccattcgttgtg
29		aagttgttaggctgttatttctattatactatgttgtagtaataagtgcattgttgtacc
30		agaagctatgatcataactataggttgatccttcatgtatcagtttgatgttgagaatac
31		tttgaattaaaagtctttttttatttttttaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
32		>seq2
33		aaacaaaccaaatatggattttattgtagccatatttgctctgtttgttattagctcatt
34		cacaattacttccacaaatgcagttgaagcttctactcttcttgacataggtaacctgag
35		tcggagcagttttcctcgtggcttcatctttggtgctggatcttcagcataccaatttga
36		aggtgcagtaaacgaaggcggtagaggaccaagtatttgggataccttcacccataaata
37		tccagaaaaaataagggatggaagcaatgcagacatcacggttgaccaatatcaccgcta
38		caaggaagatgttgggattatgaaggatcaaaatatggattcgtatagattctcaatctc
39		ttggccaagaatactcccaaagggaaagttgagcggaggcataaatcacgaaggaatcaa
40		atattacaacaaccttatcaacgaactattggctaacggtatacaaccatttgtaactct
41		ttttcattgggatcttccccaagtcttagaagatgagtatggtggtttcttaaactccgg
42		tgtaataaatgattttcgagactatacggatctttgcttcaaggaatttggagatagagt
43		gaggtattggagtactctaaatgagccatgggtgtttagcaattctggatatgcactagg
44		aacaaatgcaccaggtcgatgttcggcctccaacgtggccaagcctggtgattctggaac
45		aggaccttatatagttacacacaatcaaattcttgctcatgcagaagctgtacatgtgta
46		taagactaaataccaggcatatcaaaagggaaagataggcataacgttggtatctaactg
47		gttaatgccacttgatgataatagcataccagatataaaggctgccgagagatcacttga
48		cttccaatttggattgtttatggaacaattaacaacaggagattattctaagagcatgcg
49		gcgtatagttaaaaaccgattacctaagttctcaaaattcgaatcaagcctagtgaatgg
50		ttcatttgattttattggtataaactattactcttctagttatattagcaatgccccttc
51		acatggcaatgccaaacccagttactcaacaaatcctatgaccaatatttcatttgaaaa
52		acatgggatacccttaggtccaagggctgcttcaatttggatatatgtttatccatatat
53		gtttatccaagaggacttcgagatcttttgttacatattaaaaataaatataacaatcct
54		gcaattttcaatcactgaaaatggtatgaatgaattcaacgatgcaacacttccagtaga
55		agaagctcttttgaatacttacagaattgattactattaccgtcacttatactacattcg
56		ttctgcaatcagggctggctcaaatgtgaagggtttttacgcatggtcatttttggactg
57		taatgaatggtttgcaggctttactgttcgttttggattaaactttgtagattagaaaga
58		tggattaaaaaggtaccctaagctttctgcccaatggtacaagaactttctcaaaagaaa
59		ctagctagtattattaaaagaactttgtagtagattacagtacatcgtttgaagttgagt
60		tggtgcacctaattaaataaaagaggttactcttaacatatttttaggccattcgttgtg
61		aagttgttaggctgttatttctattatactatgttgtagtaataagtgcattgttgtacc
62		agaagctatgatcataactataggttgatccttcatgtatcagtttgatgttgagaatac
63		tttgaattaaaagtctttttttatttttttaaaaaaaaaaaaaaaaaaaaccccccccc

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~~pyfastaq/tests/data/sequences_test.fa~~ less more

0		>1
1		ACGTA
2		>2
3		A
4
5		C
6		GT
7
8		A
9
10		>3
11
12
13		ACGTA
14		>4
15		ACGTA
16
17
18

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~~pyfastaq/tests/data/sequences_test.fa.ids~~ less more

0		1
1		2
2		3
3		4

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-17

~~pyfastaq/tests/data/sequences_test.fa.qual~~ less more

0		>1
1		40 40 40
2		40 40
3
4		>2
5		40
6		40
7
8		40
9		40 40
10		>3
11
12		40 40 40 40 40
13
14		>4
15		40 40 40 40 40
16

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~~pyfastaq/tests/data/sequences_test.fa.qual.bad~~ less more

0		>1
1		40 40 40
2		40 40
3
4		>3
5		40
6		40
7
8		40
9		40 40
10		>3
11
12		40 40 40 40 40
13
14		>4
15		40 40 40 40 40
16

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~~pyfastaq/tests/data/sequences_test.fasta_to_fastq.fq~~ less more

0		@1
1		ACGTA
2		+
3		IIIII
4		@2
5		ACGTA
6		+
7		IIIII
8		@3
9		ACGTA
10		+
11		IIIII
12		@4
13		ACGTA
14		+
15		IIIII

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~~pyfastaq/tests/data/sequences_test.gbk~~ less more

0		LOCUS NAME1 5028 bp DNA PLN 21-JUN-1999
1		DEFINITION Saccharomyces cerevisiae TCP1-beta gene, partial cds, and Axl2p
2		(AXL2) and Rev7p (REV7) genes, complete cds.
3		ACCESSION U49845
4		VERSION U49845.1 GI:1293613
5		KEYWORDS .
6		SOURCE Saccharomyces cerevisiae (baker's yeast)
7		ORGANISM Saccharomyces cerevisiae
8		Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes;
9		Saccharomycetales; Saccharomycetaceae; Saccharomyces.
10		REFERENCE 1 (bases 1 to 5028)
11		AUTHORS Torpey,L.E., Gibbs,P.E., Nelson,J. and Lawrence,C.W.
12		TITLE Cloning and sequence of REV7, a gene whose function is required for
13		DNA damage-induced mutagenesis in Saccharomyces cerevisiae
14		JOURNAL Yeast 10 (11), 1503-1509 (1994)
15		PUBMED 7871890
16		REFERENCE 2 (bases 1 to 5028)
17		AUTHORS Roemer,T., Madden,K., Chang,J. and Snyder,M.
18		TITLE Selection of axial growth sites in yeast requires Axl2p, a novel
19		plasma membrane glycoprotein
20		JOURNAL Genes Dev. 10 (7), 777-793 (1996)
21		PUBMED 8846915
22		REFERENCE 3 (bases 1 to 5028)
23		AUTHORS Roemer,T.
24		TITLE Direct Submission
25		JOURNAL Submitted (22-FEB-1996) Terry Roemer, Biology, Yale University, New
26		Haven, CT, USA
27		FEATURES Location/Qualifiers
28		source 1..5028
29		/organism="Saccharomyces cerevisiae"
30		/db_xref="taxon:4932"
31		/chromosome="IX"
32		/map="9"
33		CDS <1..206
34		/codon_start=3
35		/product="TCP1-beta"
36		/protein_id="AAA98665.1"
37		/db_xref="GI:1293614"
38		/translation="SSIYNGISTSGLDLNNGTIADMRQLGIVESYKLKRAVVSSASEA
39		AEVLLRVDNIIRARPRTANRQHM"
40		gene 687..3158
41		/gene="AXL2"
42		CDS 687..3158
43		/gene="AXL2"
44		/note="plasma membrane glycoprotein"
45		/codon_start=1
46		/function="required for axial budding pattern of S.
47		cerevisiae"
48		/product="Axl2p"
49		/protein_id="AAA98666.1"
50		/db_xref="GI:1293615"
51		/translation="MTQLQISLLLTATISLLHLVVATPYEAYPIGKQYPPVARVNESF
52		TFQISNDTYKSSVDKTAQITYNCFDLPSWLSFDSSSRTFSGEPSSDLLSDANTTLYFN
53		VILEGTDSADSTSLNNTYQFVVTNRPSISLSSDFNLLALLKNYGYTNGKNALKLDPNE
54		VFNVTFDRSMFTNEESIVSYYGRSQLYNAPLPNWLFFDSGELKFTGTAPVINSAIAPE
55		TSYSFVIIATDIEGFSAVEVEFELVIGAHQLTTSIQNSLIINVTDTGNVSYDLPLNYV
56		YLDDDPISSDKLGSINLLDAPDWVALDNATISGSVPDELLGKNSNPANFSVSIYDTYG
57		DVIYFNFEVVSTTDLFAISSLPNINATRGEWFSYYFLPSQFTDYVNTNVSLEFTNSSQ
58		DHDWVKFQSSNLTLAGEVPKNFDKLSLGLKANQGSQSQELYFNIIGMDSKITHSNHSA
59		NATSTRSSHHSTSTSSYTSSTYTAKISSTSAAATSSAPAALPAANKTSSHNKKAVAIA
60		CGVAIPLGVILVALICFLIFWRRRRENPDDENLPHAISGPDLNNPANKPNQENATPLN
61		NPFDDDASSYDDTSIARRLAALNTLKLDNHSATESDISSVDEKRDSLSGMNTYNDQFQ
62		SQSKEELLAKPPVQPPESPFFDPQNRSSSVYMDSEPAVNKSWRYTGNLSPVSDIVRDS
63		YGSQKTVDTEKLFDLEAPEKEKRTSRDVTMSSLDPWNSNISPSPVRKSVTPSPYNVTK
64		HRNRHLQNIQDSQSGKNGITPTTMSTSSSDDFVPVKDGENFCWVHSMEPDRRPSKKRL
65		VDFSNKSNVNVGQVKDIHGRIPEML"
66		gene complement(3300..4037)
67		/gene="REV7"
68		CDS complement(3300..4037)
69		/gene="REV7"
70		/codon_start=1
71		/product="Rev7p"
72		/protein_id="AAA98667.1"
73		/db_xref="GI:1293616"
74		/translation="MNRWVEKWLRVYLKCYINLILFYRNVYPPQSFDYTTYQSFNLPQ
75		FVPINRHPALIDYIEELILDVLSKLTHVYRFSICIINKKNDLCIEKYVLDFSELQHVD
76		KDDQIITETEVFDEFRSSLNSLIMHLEKLPKVNDDTITFEAVINAIELELGHKLDRNR
77		RVDSLEEKAEIERDSNWVKCQEDENLPDNNGFQPPKIKLTSLVGSDVGPLIIHQFSEK
78		LISGDDKILNGVYSQYEEGESIFGSLF"
79		ORIGIN
80		1 gatcctccat atacaacggt atctccacct caggtttaga tctcaacaac ggaaccattg
81		61 ccgacatgag acagttaggt atcgtcgaga gttacaagct aaaacgagca gtagtcagct
82		121 ctgcatctga agccgctgaa gttctactaa gggtggataa catcatccgt gcaagaccaa
83		181 tgccatgact cagattctaa ttttaagcta ttcaatttct ctttgatc
84		//
85		LOCUS NAME2 5028 bp DNA PLN 21-JUN-1999
86		DEFINITION Saccharomyces cerevisiae TCP1-beta gene, partial cds, and Axl2p
87		(AXL2) and Rev7p (REV7) genes, complete cds.
88		ACCESSION U49845
89		VERSION U49845.1 GI:1293613
90		KEYWORDS .
91		SOURCE Saccharomyces cerevisiae (baker's yeast)
92		ORGANISM Saccharomyces cerevisiae
93		Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes;
94		Saccharomycetales; Saccharomycetaceae; Saccharomyces.
95		REFERENCE 1 (bases 1 to 5028)
96		AUTHORS Torpey,L.E., Gibbs,P.E., Nelson,J. and Lawrence,C.W.
97		TITLE Cloning and sequence of REV7, a gene whose function is required for
98		DNA damage-induced mutagenesis in Saccharomyces cerevisiae
99		JOURNAL Yeast 10 (11), 1503-1509 (1994)
100		PUBMED 7871890
101		REFERENCE 2 (bases 1 to 5028)
102		AUTHORS Roemer,T., Madden,K., Chang,J. and Snyder,M.
103		TITLE Selection of axial growth sites in yeast requires Axl2p, a novel
104		plasma membrane glycoprotein
105		JOURNAL Genes Dev. 10 (7), 777-793 (1996)
106		PUBMED 8846915
107		REFERENCE 3 (bases 1 to 5028)
108		AUTHORS Roemer,T.
109		TITLE Direct Submission
110		JOURNAL Submitted (22-FEB-1996) Terry Roemer, Biology, Yale University, New
111		Haven, CT, USA
112		FEATURES Location/Qualifiers
113		source 1..5028
114		/organism="Saccharomyces cerevisiae"
115		/db_xref="taxon:4932"
116		/chromosome="IX"
117		/map="9"
118		CDS <1..206
119		/codon_start=3
120		/product="TCP1-beta"
121		/protein_id="AAA98665.1"
122		/db_xref="GI:1293614"
123		/translation="SSIYNGISTSGLDLNNGTIADMRQLGIVESYKLKRAVVSSASEA
124		AEVLLRVDNIIRARPRTANRQHM"
125		gene 687..3158
126		/gene="AXL2"
127		CDS 687..3158
128		/gene="AXL2"
129		/note="plasma membrane glycoprotein"
130		/codon_start=1
131		/function="required for axial budding pattern of S.
132		cerevisiae"
133		/product="Axl2p"
134		/protein_id="AAA98666.1"
135		/db_xref="GI:1293615"
136		/translation="MTQLQISLLLTATISLLHLVVATPYEAYPIGKQYPPVARVNESF
137		TFQISNDTYKSSVDKTAQITYNCFDLPSWLSFDSSSRTFSGEPSSDLLSDANTTLYFN
138		VILEGTDSADSTSLNNTYQFVVTNRPSISLSSDFNLLALLKNYGYTNGKNALKLDPNE
139		VFNVTFDRSMFTNEESIVSYYGRSQLYNAPLPNWLFFDSGELKFTGTAPVINSAIAPE
140		TSYSFVIIATDIEGFSAVEVEFELVIGAHQLTTSIQNSLIINVTDTGNVSYDLPLNYV
141		YLDDDPISSDKLGSINLLDAPDWVALDNATISGSVPDELLGKNSNPANFSVSIYDTYG
142		DVIYFNFEVVSTTDLFAISSLPNINATRGEWFSYYFLPSQFTDYVNTNVSLEFTNSSQ
143		DHDWVKFQSSNLTLAGEVPKNFDKLSLGLKANQGSQSQELYFNIIGMDSKITHSNHSA
144		NATSTRSSHHSTSTSSYTSSTYTAKISSTSAAATSSAPAALPAANKTSSHNKKAVAIA
145		CGVAIPLGVILVALICFLIFWRRRRENPDDENLPHAISGPDLNNPANKPNQENATPLN
146		NPFDDDASSYDDTSIARRLAALNTLKLDNHSATESDISSVDEKRDSLSGMNTYNDQFQ
147		SQSKEELLAKPPVQPPESPFFDPQNRSSSVYMDSEPAVNKSWRYTGNLSPVSDIVRDS
148		YGSQKTVDTEKLFDLEAPEKEKRTSRDVTMSSLDPWNSNISPSPVRKSVTPSPYNVTK
149		HRNRHLQNIQDSQSGKNGITPTTMSTSSSDDFVPVKDGENFCWVHSMEPDRRPSKKRL
150		VDFSNKSNVNVGQVKDIHGRIPEML"
151		gene complement(3300..4037)
152		/gene="REV7"
153		CDS complement(3300..4037)
154		/gene="REV7"
155		/codon_start=1
156		/product="Rev7p"
157		/protein_id="AAA98667.1"
158		/db_xref="GI:1293616"
159		/translation="MNRWVEKWLRVYLKCYINLILFYRNVYPPQSFDYTTYQSFNLPQ
160		FVPINRHPALIDYIEELILDVLSKLTHVYRFSICIINKKNDLCIEKYVLDFSELQHVD
161		KDDQIITETEVFDEFRSSLNSLIMHLEKLPKVNDDTITFEAVINAIELELGHKLDRNR
162		RVDSLEEKAEIERDSNWVKCQEDENLPDNNGFQPPKIKLTSLVGSDVGPLIIHQFSEK
163		LISGDDKILNGVYSQYEEGESIFGSLF"
164		ORIGIN
165		1 gatcctccat atacaacggt atctccacct caggtttaga tctcaacaac ggaaccattg
166		61 ccgacatgag acagttaggt atcgtcgaga gttacaagct aaaacgagca gtagtcagct
167		121 ctgcatctga agccgctgaa gttctactaa gggtggataa catcatccgt gcaagaccaa
168		181 tgccatgact cagattctaa ttttaagcta ttcaatttct ctttgaaa
169		//

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-10

~~pyfastaq/tests/data/sequences_test.gbk.to_fasta~~ less more

0		>NAME1
1		gatcctccatatacaacggtatctccacctcaggtttagatctcaacaacggaaccattg
2		ccgacatgagacagttaggtatcgtcgagagttacaagctaaaacgagcagtagtcagct
3		ctgcatctgaagccgctgaagttctactaagggtggataacatcatccgtgcaagaccaa
4		tgccatgactcagattctaattttaagctattcaatttctctttgatc
5		>NAME2
6		gatcctccatatacaacggtatctccacctcaggtttagatctcaacaacggaaccattg
7		ccgacatgagacagttaggtatcgtcgagagttacaagctaaaacgagcagtagtcagct
8		ctgcatctgaagccgctgaagttctactaagggtggataacatcatccgtgcaagaccaa
9		tgccatgactcagattctaattttaagctattcaatttctctttgaaa

+0

-12

~~pyfastaq/tests/data/sequences_test.line_length3.fa~~ less more

0		>1
1		ACG
2		TA
3		>2
4		ACG
5		TA
6		>3
7		ACG
8		TA
9		>4
10		ACG
11		TA

+0

-6

~~pyfastaq/tests/data/sequences_test.to_fasta.strip_after_whitespace_non_unique.in.fa~~ less more

0		>1 spam
1		ACGT
2		>1 eggs
3		A
4		>2
5		GTTTG

+0

-6

~~pyfastaq/tests/data/sequences_test.to_fasta.strip_after_whitespace_non_unique.out.fa~~ less more

0		>1
1		ACGT
2		>1
3		A
4		>2
5		GTTTG

+0

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~~pyfastaq/tests/data/sequences_test.to_fasta.strip_after_whitespace_unique.in.fa~~ less more

0		>1 abcde
1		ACGT
2		>2 abcde
3		G
4		>3 hello
5		GTACCA

+0

-6

~~pyfastaq/tests/data/sequences_test.to_fasta.strip_after_whitespace_unique.out.fa~~ less more

0		>1
1		ACGT
2		>2
3		G
4		>3
5		GTACCA

+0

-4

~~pyfastaq/tests/data/test_acgtn_only.expected.fa~~ less more

0		>seq1
1		acgtACGTnN
2		>seq2
3		aNcNgNNT

+0

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~~pyfastaq/tests/data/test_acgtn_only.in.fa~~ less more

0		>seq1
1		acgtACGTnN
2		>seq2
3		aXcRg.?T

+20

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pyfastaq/tests/tasks_test.py less more

2	2	import sys
3	3	import filecmp
4	4	import os
	5	import tempfile
5	6	import unittest
6	7	from pyfastaq import tasks, sequences
7	8

171	172	self.assertTrue(filecmp.cmp(correct_files[i], outfile))
172	173	os.unlink(outfile)
173	174
	175	def test_regex_check_comments_filter(self):
	176	'''When check_comments is true, and the regex is in the comment'''
	177	infile = tempfile.NamedTemporaryFile(suffix=".fa", mode="w+")
	178	infile.write(
	179	">read1 foo=bar\nAGCT\n>read2 bar=foo\nGGG\n>read3\nGGGG\n>read4 foo=ba\n"
	180	"GCA\n>read5foo=bar\nGCAT"
	181	)
	182	infile.seek(0)
	183	regex = '\sfoo=bar'
	184	outfile = tempfile.NamedTemporaryFile(suffix=".fa", mode="w+")
	185
	186	tasks.filter(infile.name, outfile.name, regex=regex, check_comments=True)
	187	with open(outfile.name) as handle:
	188	actual = handle.read()
	189
	190	expected = ">read1 foo=bar\nAGCT\n"
	191
	192	self.assertEqual(actual, expected)
	193
174	194	def test_ids_from_file_filter(self):
175	195	'''Test that can extract reads from a file of read names'''
176	196	infile = os.path.join(data_dir, 'sequences_test_filter_by_ids_file.fa')

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pyfastaq.egg-info/PKG-INFO less more

	0	Metadata-Version: 2.1
	1	Name: pyfastaq
	2	Version: 3.17.0
	3	Summary: Script to manipulate FASTA and FASTQ files, plus API for developers
	4	Home-page: https://github.com/sanger-pathogens/Fastaq
	5	Author: Martin Hunt
	6	Author-email: path-help@sanger.ac.uk
	7	License: GPLv3
	8	Platform: UNKNOWN
	9	Classifier: Development Status :: 4 - Beta
	10	Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
	11	Classifier: Programming Language :: Python :: 3 :: Only
	12	Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
	13	License-File: LICENSE
	14	License-File: AUTHORS
	15
	16	UNKNOWN
	17

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pyfastaq.egg-info/SOURCES.txt less more

	0	AUTHORS
	1	LICENSE
	2	MANIFEST.in
	3	README.md
	4	setup.py
	5	pyfastaq/__init__.py
	6	pyfastaq/caf.py
	7	pyfastaq/genetic_codes.py
	8	pyfastaq/intervals.py
	9	pyfastaq/sequences.py
	10	pyfastaq/tasks.py
	11	pyfastaq/utils.py
	12	pyfastaq.egg-info/PKG-INFO
	13	pyfastaq.egg-info/SOURCES.txt
	14	pyfastaq.egg-info/dependency_links.txt
	15	pyfastaq.egg-info/top_level.txt
	16	pyfastaq/runners/__init__.py
	17	pyfastaq/runners/acgtn_only.py
	18	pyfastaq/runners/add_indels.py
	19	pyfastaq/runners/caf_to_fastq.py
	20	pyfastaq/runners/capillary_to_pairs.py
	21	pyfastaq/runners/chunker.py
	22	pyfastaq/runners/count_sequences.py
	23	pyfastaq/runners/deinterleave.py
	24	pyfastaq/runners/enumerate_names.py
	25	pyfastaq/runners/expand_nucleotides.py
	26	pyfastaq/runners/fasta_to_fastq.py
	27	pyfastaq/runners/filter.py
	28	pyfastaq/runners/get_ids.py
	29	pyfastaq/runners/get_seq_flanking_gaps.py
	30	pyfastaq/runners/interleave.py
	31	pyfastaq/runners/make_random_contigs.py
	32	pyfastaq/runners/merge.py
	33	pyfastaq/runners/replace_bases.py
	34	pyfastaq/runners/reverse_complement.py
	35	pyfastaq/runners/scaffolds_to_contigs.py
	36	pyfastaq/runners/search_for_seq.py
	37	pyfastaq/runners/sequence_trim.py
	38	pyfastaq/runners/sort_by_name.py
	39	pyfastaq/runners/sort_by_size.py
	40	pyfastaq/runners/split_by_base_count.py
	41	pyfastaq/runners/strip_illumina_suffix.py
	42	pyfastaq/runners/to_boulderio.py
	43	pyfastaq/runners/to_fake_qual.py
	44	pyfastaq/runners/to_fasta.py
	45	pyfastaq/runners/to_mira_xml.py
	46	pyfastaq/runners/to_orfs_gff.py
	47	pyfastaq/runners/to_perfect_reads.py
	48	pyfastaq/runners/to_random_subset.py
	49	pyfastaq/runners/to_tiling_bam.py
	50	pyfastaq/runners/to_unique_by_id.py
	51	pyfastaq/runners/translate.py
	52	pyfastaq/runners/trim_Ns_at_end.py
	53	pyfastaq/runners/trim_contigs.py
	54	pyfastaq/runners/trim_ends.py
	55	pyfastaq/runners/version.py
	56	pyfastaq/tests/caf_test.py
	57	pyfastaq/tests/intervals_test.py
	58	pyfastaq/tests/sequences_test.py
	59	pyfastaq/tests/tasks_test.py
	60	pyfastaq/tests/utils_test.py
	61	pyfastaq/tests/data/sequences_test_3-per-line.fa
	62	pyfastaq/tests/data/sequences_test_cap_to_read_pairs.fa
	63	pyfastaq/tests/data/sequences_test_cap_to_read_pairs.fa.paired.gz
	64	pyfastaq/tests/data/sequences_test_cap_to_read_pairs.fa.unpaired.gz
	65	pyfastaq/tests/data/sequences_test_deinterleaved_1.fa
	66	pyfastaq/tests/data/sequences_test_deinterleaved_2.fa
	67	pyfastaq/tests/data/sequences_test_deinterleaved_bad2_1.fa
	68	pyfastaq/tests/data/sequences_test_deinterleaved_bad2_2.fa
	69	pyfastaq/tests/data/sequences_test_deinterleaved_bad_1.fa
	70	pyfastaq/tests/data/sequences_test_deinterleaved_bad_2.fa
	71	pyfastaq/tests/data/sequences_test_deinterleaved_no_suffixes_1.fa
	72	pyfastaq/tests/data/sequences_test_deinterleaved_no_suffixes_2.fa
	73	pyfastaq/tests/data/sequences_test_empty_file
	74	pyfastaq/tests/data/sequences_test_enumerate_names.fa
	75	pyfastaq/tests/data/sequences_test_enumerate_names.fa.out.add_suffix
	76	pyfastaq/tests/data/sequences_test_enumerate_names.fa.out.keep_suffix
	77	pyfastaq/tests/data/sequences_test_enumerate_names.fa.out.start.1
	78	pyfastaq/tests/data/sequences_test_enumerate_names.fa.out.start.1.rename_file
	79	pyfastaq/tests/data/sequences_test_enumerate_names.fa.out.start.2
	80	pyfastaq/tests/data/sequences_test_fai_test.fa
	81	pyfastaq/tests/data/sequences_test_fai_test.fa.fai
	82	pyfastaq/tests/data/sequences_test_fail_no_AT.fq
	83	pyfastaq/tests/data/sequences_test_fail_no_plus.fq
	84	pyfastaq/tests/data/sequences_test_fail_no_qual.fq
	85	pyfastaq/tests/data/sequences_test_fail_no_seq.fq
	86	pyfastaq/tests/data/sequences_test_fastaq_replace_bases.expected.fa
	87	pyfastaq/tests/data/sequences_test_fastaq_replace_bases.fa
	88	pyfastaq/tests/data/sequences_test_filter_by_ids_file.fa
	89	pyfastaq/tests/data/sequences_test_filter_by_ids_file.fa.filtered
	90	pyfastaq/tests/data/sequences_test_filter_by_ids_file.fa.filtered.invert
	91	pyfastaq/tests/data/sequences_test_filter_by_ids_file.fa.ids
	92	pyfastaq/tests/data/sequences_test_filter_by_regex.fa
	93	pyfastaq/tests/data/sequences_test_filter_by_regex.first-char-a.fa
	94	pyfastaq/tests/data/sequences_test_filter_by_regex.first-of-pair.fa
	95	pyfastaq/tests/data/sequences_test_filter_by_regex.numeric.fa
	96	pyfastaq/tests/data/sequences_test_get_seqs_flanking_gaps.fa
	97	pyfastaq/tests/data/sequences_test_get_seqs_flanking_gaps.fa.out
	98	pyfastaq/tests/data/sequences_test_gffv3.gff
	99	pyfastaq/tests/data/sequences_test_gffv3.gff.fasta
	100	pyfastaq/tests/data/sequences_test_gffv3.gff.to_fasta
	101	pyfastaq/tests/data/sequences_test_gffv3.no_FASTA_line.gff
	102	pyfastaq/tests/data/sequences_test_gffv3.no_FASTA_line.gff.to_fasta
	103	pyfastaq/tests/data/sequences_test_gffv3.no_seq.2.gff
	104	pyfastaq/tests/data/sequences_test_gffv3.no_seq.gff
	105	pyfastaq/tests/data/sequences_test_good_file.fq
	106	pyfastaq/tests/data/sequences_test_good_file.fq.to_fasta
	107	pyfastaq/tests/data/sequences_test_good_file_mira.xml
	108	pyfastaq/tests/data/sequences_test_interleaved.fa
	109	pyfastaq/tests/data/sequences_test_interleaved.fq
	110	pyfastaq/tests/data/sequences_test_interleaved_bad.fa
	111	pyfastaq/tests/data/sequences_test_interleaved_with_suffixes.fa
	112	pyfastaq/tests/data/sequences_test_length_filter.fa
	113	pyfastaq/tests/data/sequences_test_length_filter.min-0.max-1.fa
	114	pyfastaq/tests/data/sequences_test_length_filter.min-0.max-inf.fa
	115	pyfastaq/tests/data/sequences_test_length_filter.min-4.max-4.fa
	116	pyfastaq/tests/data/sequences_test_make_random_contigs.default.fa
	117	pyfastaq/tests/data/sequences_test_make_random_contigs.first-42.fa
	118	pyfastaq/tests/data/sequences_test_make_random_contigs.name-by-letters.fa
	119	pyfastaq/tests/data/sequences_test_make_random_contigs.prefix-p.fa
	120	pyfastaq/tests/data/sequences_test_merge_to_one_seq.fa
	121	pyfastaq/tests/data/sequences_test_merge_to_one_seq.fq
	122	pyfastaq/tests/data/sequences_test_merge_to_one_seq.merged.fa
	123	pyfastaq/tests/data/sequences_test_merge_to_one_seq.merged.fq
	124	pyfastaq/tests/data/sequences_test_not_a_fastaq_file
	125	pyfastaq/tests/data/sequences_test_one-per-line.fa
	126	pyfastaq/tests/data/sequences_test_orfs.fa
	127	pyfastaq/tests/data/sequences_test_orfs.gff
	128	pyfastaq/tests/data/sequences_test_phylip.interleaved
	129	pyfastaq/tests/data/sequences_test_phylip.interleaved.to_fasta
	130	pyfastaq/tests/data/sequences_test_phylip.interleaved2
	131	pyfastaq/tests/data/sequences_test_phylip.interleaved2.to_fasta
	132	pyfastaq/tests/data/sequences_test_phylip.made_by_seaview
	133	pyfastaq/tests/data/sequences_test_phylip.made_by_seaview.to_fasta
	134	pyfastaq/tests/data/sequences_test_phylip.sequential
	135	pyfastaq/tests/data/sequences_test_phylip.sequential.to_fasta
	136	pyfastaq/tests/data/sequences_test_revcomp.fa
	137	pyfastaq/tests/data/sequences_test_search_string.fa
	138	pyfastaq/tests/data/sequences_test_search_string.fa.hits
	139	pyfastaq/tests/data/sequences_test_split_fixed_size.fa
	140	pyfastaq/tests/data/sequences_test_split_fixed_size.fa.split.1
	141	pyfastaq/tests/data/sequences_test_split_fixed_size.fa.split.2
	142	pyfastaq/tests/data/sequences_test_split_fixed_size.fa.split.3
	143	pyfastaq/tests/data/sequences_test_split_fixed_size.fa.split.4
	144	pyfastaq/tests/data/sequences_test_split_fixed_size.fa.split.5
	145	pyfastaq/tests/data/sequences_test_split_fixed_size.fa.split.6
	146	pyfastaq/tests/data/sequences_test_split_fixed_size.fa.split.coords
	147	pyfastaq/tests/data/sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.1
	148	pyfastaq/tests/data/sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.2
	149	pyfastaq/tests/data/sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.3
	150	pyfastaq/tests/data/sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.4
	151	pyfastaq/tests/data/sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.coords
	152	pyfastaq/tests/data/sequences_test_split_fixed_size_onefile.fa
	153	pyfastaq/tests/data/sequences_test_split_fixed_size_onefile.out.fa
	154	pyfastaq/tests/data/sequences_test_split_fixed_size_onefile.skip_Ns.out.fa
	155	pyfastaq/tests/data/sequences_test_split_test.fa
	156	pyfastaq/tests/data/sequences_test_split_test.fa.2.1
	157	pyfastaq/tests/data/sequences_test_split_test.fa.2.2
	158	pyfastaq/tests/data/sequences_test_split_test.fa.2.3
	159	pyfastaq/tests/data/sequences_test_split_test.fa.2.4
	160	pyfastaq/tests/data/sequences_test_split_test.fa.3.1
	161	pyfastaq/tests/data/sequences_test_split_test.fa.3.2
	162	pyfastaq/tests/data/sequences_test_split_test.fa.3.3
	163	pyfastaq/tests/data/sequences_test_split_test.fa.4.1
	164	pyfastaq/tests/data/sequences_test_split_test.fa.4.2
	165	pyfastaq/tests/data/sequences_test_split_test.fa.4.3
	166	pyfastaq/tests/data/sequences_test_split_test.fa.6.1
	167	pyfastaq/tests/data/sequences_test_split_test.fa.6.2
	168	pyfastaq/tests/data/sequences_test_split_test.fa.6.limit2.1
	169	pyfastaq/tests/data/sequences_test_split_test.fa.6.limit2.2
	170	pyfastaq/tests/data/sequences_test_split_test.fa.6.limit2.3
	171	pyfastaq/tests/data/sequences_test_split_test.long.fa
	172	pyfastaq/tests/data/sequences_test_split_test.long.fa.2.1
	173	pyfastaq/tests/data/sequences_test_split_test.long.fa.2.2
	174	pyfastaq/tests/data/sequences_test_strip_after_whitespace.fa
	175	pyfastaq/tests/data/sequences_test_strip_after_whitespace.fa.to_fasta
	176	pyfastaq/tests/data/sequences_test_strip_illumina_suffix.fq
	177	pyfastaq/tests/data/sequences_test_strip_illumina_suffix.fq.stripped
	178	pyfastaq/tests/data/sequences_test_to_fasta_union.in.fa
	179	pyfastaq/tests/data/sequences_test_to_fasta_union.out.fa
	180	pyfastaq/tests/data/sequences_test_to_unique_by_id.fa
	181	pyfastaq/tests/data/sequences_test_to_unique_by_id.fa.out
	182	pyfastaq/tests/data/sequences_test_translate.fa
	183	pyfastaq/tests/data/sequences_test_translate.fa.frame0
	184	pyfastaq/tests/data/sequences_test_translate.fa.frame1
	185	pyfastaq/tests/data/sequences_test_translate.fa.frame2
	186	pyfastaq/tests/data/sequences_test_trim_Ns_at_end.fa
	187	pyfastaq/tests/data/sequences_test_trim_Ns_at_end.fa.trimmed
	188	pyfastaq/tests/data/sequences_test_trim_contigs.fa
	189	pyfastaq/tests/data/sequences_test_trim_contigs.fa.out
	190	pyfastaq/tests/data/sequences_test_trimmed.fq
	191	pyfastaq/tests/data/sequences_test_untrimmed.fq
	192	pyfastaq/tests/data/tasks_test_expend_nucleotides.in.fa
	193	pyfastaq/tests/data/tasks_test_expend_nucleotides.in.fq
	194	pyfastaq/tests/data/tasks_test_expend_nucleotides.out.fa
	195	pyfastaq/tests/data/tasks_test_expend_nucleotides.out.fq
	196	pyfastaq/tests/data/tasks_test_fasta_to_fake_qual.in.fa
	197	pyfastaq/tests/data/tasks_test_fasta_to_fake_qual.out.default.qual
	198	pyfastaq/tests/data/tasks_test_fasta_to_fake_qual.out.q42.qual
	199	pyfastaq/tests/data/tasks_test_filter_paired_both_pass.in_1.fa
	200	pyfastaq/tests/data/tasks_test_filter_paired_both_pass.in_2.fa
	201	pyfastaq/tests/data/tasks_test_filter_paired_both_pass.out_1.fa
	202	pyfastaq/tests/data/tasks_test_filter_paired_both_pass.out_2.fa
	203	pyfastaq/tests/data/tasks_test_filter_paired_one_pass.in_1.fa
	204	pyfastaq/tests/data/tasks_test_filter_paired_one_pass.in_2.fa
	205	pyfastaq/tests/data/tasks_test_filter_paired_one_pass.out_1.fa
	206	pyfastaq/tests/data/tasks_test_filter_paired_one_pass.out_2.fa
	207	pyfastaq/tests/data/tasks_test_length_offsets_from_fai.fa
	208	pyfastaq/tests/data/tasks_test_length_offsets_from_fai.fa.fai
	209	pyfastaq/tests/data/tasks_test_make_long_reads.input.fa
	210	pyfastaq/tests/data/tasks_test_make_long_reads.output.fa
	211	pyfastaq/tests/data/tasks_test_mean_length.fa
	212	pyfastaq/tests/data/tasks_test_sequence_trim_1.fa
	213	pyfastaq/tests/data/tasks_test_sequence_trim_1.trimmed.fa
	214	pyfastaq/tests/data/tasks_test_sequence_trim_2.fa
	215	pyfastaq/tests/data/tasks_test_sequence_trim_2.trimmed.fa
	216	pyfastaq/tests/data/tasks_test_sequences_to_trim.fa
	217	pyfastaq/tests/data/tasks_test_sort_by_name.in.fa
	218	pyfastaq/tests/data/tasks_test_sort_by_name.out.fa
	219	pyfastaq/tests/data/tasks_test_sort_by_size.in.fa
	220	pyfastaq/tests/data/tasks_test_sort_by_size.out.fa
	221	pyfastaq/tests/data/tasks_test_sort_by_size.out.rev.fa
	222	pyfastaq/tests/data/tasks_test_stats_from_fai.in.empty.fai
	223	pyfastaq/tests/data/tasks_test_stats_from_fai.in.fai
	224	pyfastaq/tests/data/tasks_test_to_boulderio.in.fa
	225	pyfastaq/tests/data/tasks_test_to_boulderio.out.boulder
	226	pyfastaq/tests/data/tasks_test_to_fastg.fasta
	227	pyfastaq/tests/data/tasks_test_to_fastg.fastg
	228	pyfastaq/tests/data/tasks_test_to_fastg.ids_to_circularise
	229	pyfastaq/tests/data/utils_test_file_transpose.txt
	230	pyfastaq/tests/data/utils_test_file_transposed.txt
	231	pyfastaq/tests/data/utils_test_not_really_zipped.gz
	232	pyfastaq/tests/data/utils_test_scaffolds.fa
	233	pyfastaq/tests/data/utils_test_scaffolds.fa.to_contigs.fa
	234	pyfastaq/tests/data/utils_test_scaffolds.fa.to_contigs.number_contigs.fa
	235	pyfastaq/tests/data/utils_test_system_call.txt
	236	scripts/fastaq⏎

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pyfastaq.egg-info/dependency_links.txt less more

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pyfastaq

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setup.cfg less more

	0	[egg_info]
	1	tag_build =
	2	tag_date = 0
	3